Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate 3607958 Dshi_1366 aminotransferase class-III (RefSeq)
Query= curated2:Q8TUZ5 (389 letters) >FitnessBrowser__Dino:3607958 Length = 441 Score = 191 bits (486), Expect = 3e-53 Identities = 134/413 (32%), Positives = 208/413 (50%), Gaps = 46/413 (11%) Query: 19 PVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLIHCSNLYYNE 78 P V +G EG + +D AG+ GH P +VEA++ Q L + Sbjct: 29 PRMFVAADGMYYTTAEGRQVLDGTAGLWCCNAGHKRPRIVEAIQAQAAELDYAPAFQMGH 88 Query: 79 PQA-EAARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF------TGCTKFIAFEGGF 131 P+A E A L E AP ++ VF+ NSG+E+VE A+K+A + G T+ I E G+ Sbjct: 89 PRAFELANRLVEIAPDGMDHVFYTNSGSEAVESALKIALAYHRARGEAGRTRLIGRERGY 148 Query: 132 HGRTMGALSATWKPEFREPFEPLVPEFEHVPYGDV-----------------NAVEKAID 174 HG G +S R+ F L+ +H+P+ + + +E+ I Sbjct: 149 HGVNFGGISVGGIVNNRKHFGTLLTGVDHLPHTHIPENQWSRGMPELGAHLADDLERIIA 208 Query: 175 ----DDTAAVIVEPVQGEAGVRIPPEGFLRELRELCDEHGLLLIVDEVQSGMGRTGQFFA 230 + AAVIVEP+ G GV +PP+G+L+ LR++ +HG++LI DEV +G GR G F Sbjct: 209 LHGAETIAAVIVEPMAGSTGVLLPPKGYLQRLRKITQDHGIVLIFDEVITGFGRVGAAFG 268 Query: 231 FEHEDVLPDIVCLAKGLGGGV-PVGATIAREEVAEAFEPGD-------HGSTFGGNPLAC 282 + V PD++ AKGL GV P+GA + + +AF G HG T+ GNP+A Sbjct: 269 AQRFGVTPDMITCAKGLTNGVIPMGAVLCGSHIHDAFMQGPENLIELFHGYTYSGNPIAS 328 Query: 283 AAVCAAVSTVLEENLPEAA---ERKGKLAMRILSEAEDVVEEVRGRGLMMGVEV-----G 334 AA A + T E++L A E + A+ L A V+ ++R GL+ +E+ Sbjct: 329 AAGLATLETYREDDLFARALDLEPYWQEALHSLKGARHVI-DIRNLGLIGAIELEPISGH 387 Query: 335 DDERAKDVAREMLDRGALVNVTSGDVIRLVPPLVIGEDELEKALAELADALRA 387 +RA + D+G L+ T+GD+I L PPL+I ++++ + L + L A Sbjct: 388 PTKRAFQAFLDAYDKGVLIR-TTGDIIALSPPLIIETAQIDRIVETLGEVLAA 439 Lambda K H 0.318 0.137 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 401 Number of extensions: 21 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 389 Length of database: 441 Length adjustment: 31 Effective length of query: 358 Effective length of database: 410 Effective search space: 146780 Effective search space used: 146780 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory